Core
momapy.celldesigner.core
Classes for CellDesigner maps
Classes:
| Name | Description |
|---|---|
AndGate |
Class for and gates |
AndGateLayout |
Class for and gate layouts |
AntisenseRNA |
Class for antisense RNAs |
AntisenseRNALayout |
Class for antisense RNA layouts |
AntisenseRNATemplate |
Class for antisense RNA templates |
BooleanLogicGate |
Base class for Boolean logic gates |
Catalysis |
Class for catalyses |
CatalysisLayout |
Class for catalysis layouts |
Catalyzer |
Class for catalyzers |
CellDesignerDoubleHeadedArc |
Base class for CellDesigner double-headed arcs |
CellDesignerLayout |
Class for CellDesigner layouts |
CellDesignerMap |
Class for CellDesigner maps |
CellDesignerModel |
Class for CellDesigner models |
CellDesignerModelElement |
Base class for CellDesigner model elements |
CellDesignerNode |
Base class for CellDesigner nodes |
CellDesignerSingleHeadedArc |
Base class for CellDesigner single-headed arcs |
CodingRegion |
Class for coding regions |
Compartment |
Class for compartments |
Complex |
Class for complexes |
ComplexLayout |
Class for complex layouts |
ConsumptionLayout |
Class for consumption layouts |
Degraded |
Class for degradeds |
DegradedLayout |
Class for degraded layouts |
Dissociation |
Class for dissociations |
DissociationLayout |
Class for dissociation layouts |
Drug |
Class for drugs |
DrugLayout |
Class for drug layouts |
Gene |
Class for genes |
GeneLayout |
Class for gene layouts |
GeneTemplate |
Class for gene templates |
GenericProtein |
Class for generic proteins |
GenericProteinLayout |
Class for generic protein layouts |
GenericProteinTemplate |
Class for generic protein templates |
HeterodimerAssociation |
Class for heterodimer associations |
HeterodimerAssociationLayout |
Class for heterodimer association layouts |
Inhibition |
Class for inhibitions |
InhibitionLayout |
Class for inhibition layouts |
Inhibitor |
Class for inhibitors |
Ion |
Class for ions |
IonChannel |
Class for ion channels |
IonChannelLayout |
Class for generic ion channel layouts |
IonChannelTemplate |
Class for ion channel templates |
IonLayout |
Class for ion layouts |
KnownOrUnknownModulator |
Base class for know or unknown modulators |
KnownTransitionOmitted |
Class for known transitions omitted |
KnownTransitionOmittedLayout |
Class for known transition omitted layouts |
LogicArcLayout |
Class for logic arc layouts |
Modification |
Class for modifications |
ModificationLayout |
Class for modification layouts |
ModificationResidue |
Class for modification residues |
ModificationSite |
Class for modification sites |
ModificationState |
Class for modification states |
Modulation |
Class for modulations |
ModulationLayout |
Class for modulation layouts |
Modulator |
Class for modulators |
NegativeInfluence |
Class for negative influences |
NotGate |
Class for not gates |
NotGateLayout |
Class for not gate layouts |
OrGate |
Class for or gates |
OrGateLayout |
Class for or gate layouts |
OvalCompartmentLayout |
Class for oval compartment layouts |
Phenotype |
Class for phenotypes |
PhenotypeLayout |
Class for phenotype layouts |
PhysicalStimulation |
Class for physical stimulations |
PhysicalStimulationLayout |
Class for physical stimulation layouts |
PhysicalStimulator |
Class for physical stimulators |
PositiveInfluence |
Class for positive influences |
PositiveInfluenceLayout |
Class for positive influence layouts |
Product |
Class for products |
ProductionLayout |
Class for production layouts |
Protein |
Base class for proteins |
ProteinBindingDomain |
Class for protein binding domains |
ProteinTemplate |
Base class for protein templates |
RNA |
Class for RNAs |
RNALayout |
Class for RNA layouts |
RNATemplate |
Class for RNA templates |
Reactant |
Class for reactants |
Reaction |
Base class for reactions |
Receptor |
Class for receptors |
ReceptorLayout |
Class for receptor layouts |
ReceptorTemplate |
Class for receptor templates |
RectangleCompartmentLayout |
Class for rectangle compartment layouts |
Region |
Class for regions |
RegulatoryRegion |
Class for regulatory regions |
SimpleMolecule |
Class for simple molecules |
SimpleMoleculeLayout |
Class for simple chemical layouts |
Species |
Base class for species |
SpeciesTemplate |
Base class for species templates |
StateTransition |
Class for state transitions |
StateTransitionLayout |
Class for state transition layouts |
StructuralState |
Class for structural states |
StructuralStateLayout |
Class for structural states layouts |
Transcription |
Class for transcriptions |
TranscriptionLayout |
Class for transcription layouts |
TranscriptionStartingSiteL |
Class for left transcription starting sites |
TranscriptionStartingSiteR |
Class for right transcription starting sites |
Translation |
Class for translation |
TranslationLayout |
Class for translation layouts |
Transport |
Class for transports |
TransportLayout |
Class for transport layouts |
Trigger |
Class for triggers |
Triggering |
Class for triggerings |
TriggeringLayout |
Class for triggering layouts |
TruncatedProtein |
Class for truncated proteins |
TruncatedProteinLayout |
Class for truncated protein layouts |
TruncatedProteinTemplate |
Class for truncated protein templates |
Truncation |
Class for truncations |
TruncationLayout |
Class for truncation layouts |
Unknown |
Class for unknown species |
UnknownCatalysis |
Class for unknown catalyses |
UnknownCatalysisLayout |
Class for unknown catalysis layouts |
UnknownCatalyzer |
Class for unknown catalyzers |
UnknownGate |
Class for unknown gates |
UnknownGateLayout |
Class for unknown gate layouts |
UnknownInhibition |
Class for unknown inhibitions |
UnknownInhibitionLayout |
Class for unknown inhibition layouts |
UnknownInhibitor |
Class for unknown inhibitors |
UnknownLayout |
Class for unknown species layouts |
UnknownModulation |
Class for unknown modulations |
UnknownModulationLayout |
Class for unknown modulation layouts |
UnknownModulator |
Class for unknown modulators |
UnknownNegativeInfluence |
Class for unknown negative influences |
UnknownPhysicalStimulation |
Class for unknown physical stimulations |
UnknownPhysicalStimulationLayout |
Class for unknown physical stimulation layouts |
UnknownPositiveInfluence |
Class for unknown positive influences |
UnknownPositiveInfluenceLayout |
Class for unknown positive influence layouts |
UnknownTransition |
Class for unknown transitions |
UnknownTransitionLayout |
Class for unknown transition layouts |
UnknownTriggering |
Class for unknown triggerings |
UnknownTriggeringLayout |
Class for unknown triggering layouts |
AndGate
dataclass
AndGate(*, id_: str = make_uuid4_as_str(), inputs: frozenset[Species] = frozenset())
AndGateLayout
dataclass
AndGateLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 15.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 15.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None)
Bases: _SimpleNodeMixin, _TextMixin, CellDesignerNode
Class for and gate layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
label_center
label_center() -> Point
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
AntisenseRNA
dataclass
AntisenseRNA(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: AntisenseRNATemplate, modifications: frozenset[Modification] = frozenset())
AntisenseRNALayout
dataclass
AntisenseRNALayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, angle: float = 45.0)
Bases: _MultiNodeMixin, CellDesignerNode
Class for antisense RNA layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
angle |
float
|
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
class-attribute
instance-attribute
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/celldesigner/core.py
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/celldesigner/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/celldesigner/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/celldesigner/core.py
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/celldesigner/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/celldesigner/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/celldesigner/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/celldesigner/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/celldesigner/core.py
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/celldesigner/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/celldesigner/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/celldesigner/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/celldesigner/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/celldesigner/core.py
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/celldesigner/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/celldesigner/core.py
AntisenseRNATemplate
dataclass
AntisenseRNATemplate(*, id_: str = make_uuid4_as_str(), name: str, regions: frozenset[ModificationSite | CodingRegion | ProteinBindingDomain] = frozenset())
BooleanLogicGate
dataclass
BooleanLogicGate(*, id_: str = make_uuid4_as_str(), inputs: frozenset[Species] = frozenset())
Catalysis
dataclass
Catalysis(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
CatalysisLayout
dataclass
CatalysisLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 7.0, arrowhead_width: float = 7.0)
Bases: CellDesignerSingleHeadedArc
Class for catalysis layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
Catalyzer
dataclass
Catalyzer(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)
CellDesignerDoubleHeadedArc
dataclass
CellDesignerDoubleHeadedArc(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = None, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = None, end_arrowhead_stroke_dasharray: tuple[float, ...] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = None, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = None, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = None, start_arrowhead_stroke_dasharray: tuple[float, ...] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = None, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)
Bases: DoubleHeadedArc
Base class for CellDesigner double-headed arcs
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_bbox
Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
end_arrowhead_length
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_length
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
CellDesignerLayout
dataclass
CellDesignerLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, fill: NoneValueType | Color | None = NoneValue, filter: NoneValueType | Filter | None = None, height: float, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float)
Bases: Layout
Class for CellDesigner layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
is_sublayout |
Return |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
is_sublayout
Return true if another given layout is a sublayout of the layout, false otherwise
Source code in src/momapy/core.py
label_center
label_center() -> Point
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
CellDesignerMap
dataclass
CellDesignerMap(*, id_: str = make_uuid4_as_str(), model: CellDesignerModel | None = None, layout: CellDesignerLayout | None = None, layout_model_mapping: LayoutModelMapping | None = None)
Bases: Map
Class for CellDesigner maps
Methods:
| Name | Description |
|---|---|
get_mapping |
Return the layout elements mapped to the given model element |
is_submap |
Return |
get_mapping
get_mapping(map_element: MapElement | tuple[ModelElement, ModelElement])
Return the layout elements mapped to the given model element
is_submap
Return true if another given map is a submap of the Map, false otherwise
Source code in src/momapy/core.py
CellDesignerModel
dataclass
CellDesignerModel(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartments: frozenset[Compartment] = frozenset(), species: frozenset[Species] = frozenset(), reactions: frozenset[Reaction] = frozenset(), species_templates: frozenset[SpeciesTemplate] = frozenset(), boolean_logic_gates: frozenset[BooleanLogicGate] = frozenset(), modulations: frozenset[Modulation | UnknownModulation] = frozenset())
Bases: Model
Class for CellDesigner models
CellDesignerModelElement
dataclass
CellDesignerNode
dataclass
CellDesignerNode(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float)
Bases: SBGNNode
Base class for CellDesigner nodes
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
label_center
label_center() -> Point
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
CellDesignerSingleHeadedArc
dataclass
CellDesignerSingleHeadedArc(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = None, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)
Bases: SingleHeadedArc
Base class for CellDesigner single-headed arcs
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
CodingRegion
dataclass
Compartment
dataclass
Compartment(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, outside: Optional[ForwardRef(Compartment, module=core)] = None)
Complex
dataclass
Complex(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, structural_states: frozenset[StructuralState] = frozenset(), subunits: frozenset[Species] = frozenset())
ComplexLayout
dataclass
ComplexLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, cut_corners: float = 6.0)
Bases: _MultiNodeMixin, CellDesignerNode
Class for complex layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
ConsumptionLayout
dataclass
ConsumptionLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = None, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)
Bases: CellDesignerSingleHeadedArc
Class for consumption layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
Degraded
dataclass
DegradedLayout
dataclass
DegradedLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 30.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1)
Bases: _MultiNodeMixin, CellDesignerNode
Class for degraded layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
Dissociation
dataclass
Dissociation(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())
DissociationLayout
dataclass
DissociationLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = white, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 10.0, end_arrowhead_sep: float = 2.0, end_arrowhead_width: float = 10.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)
Bases: ReactionLayout, _ReactionNodeMixin
Class for dissociation layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_bbox
Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
end_arrowhead_length
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_length
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
Drug
dataclass
DrugLayout
dataclass
DrugLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, horizontal_proportion: float = 0.2, sep: float = 4.0)
Bases: _MultiNodeMixin, CellDesignerNode
Class for drug layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
Gene
dataclass
Gene(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: GeneTemplate, modifications: frozenset[Modification] = frozenset())
GeneLayout
dataclass
GeneLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1)
Bases: _MultiNodeMixin, CellDesignerNode
Class for gene layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
GeneTemplate
dataclass
GeneTemplate(*, id_: str = make_uuid4_as_str(), name: str, regions: frozenset[ModificationSite | CodingRegion | RegulatoryRegion | TranscriptionStartingSiteL | TranscriptionStartingSiteR] = frozenset())
GenericProtein
dataclass
GenericProtein(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: GenericProteinTemplate, modifications: frozenset[Modification] = frozenset(), structural_states: frozenset[StructuralState] = frozenset())
GenericProteinLayout
dataclass
GenericProteinLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, rounded_corners: float = 5.0)
Bases: _MultiNodeMixin, CellDesignerNode
Class for generic protein layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
GenericProteinTemplate
dataclass
GenericProteinTemplate(*, id_: str = make_uuid4_as_str(), name: str, modification_residues: frozenset[ModificationResidue] = frozenset())
HeterodimerAssociation
dataclass
HeterodimerAssociation(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())
HeterodimerAssociationLayout
dataclass
HeterodimerAssociationLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 8.0, end_arrowhead_width: float = 15.0, start_arrowhead_height: float = 6.0, start_arrowhead_width: float = 6.0)
Bases: ReactionLayout, _ReactionNodeMixin
Class for heterodimer association layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_bbox
Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
end_arrowhead_length
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_length
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
Inhibition
dataclass
Inhibition(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
InhibitionLayout
dataclass
InhibitionLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 3.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = None, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0)
Bases: CellDesignerSingleHeadedArc
Class for inhibition layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
Inhibitor
dataclass
Inhibitor(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)
Ion
dataclass
IonChannel
dataclass
IonChannel(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: IonChannelTemplate, modifications: frozenset[Modification] = frozenset(), structural_states: frozenset[StructuralState] = frozenset())
IonChannelLayout
dataclass
IonChannelLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, rounded_corners: float = 5.0, right_rectangle_width: float = 20.0)
Bases: _MultiNodeMixin, CellDesignerNode
Class for generic ion channel layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
IonChannelTemplate
dataclass
IonChannelTemplate(*, id_: str = make_uuid4_as_str(), name: str, modification_residues: frozenset[ModificationResidue] = frozenset())
IonLayout
dataclass
IonLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1)
Bases: _MultiNodeMixin, CellDesignerNode
Class for ion layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
KnownOrUnknownModulator
dataclass
KnownOrUnknownModulator(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)
KnownTransitionOmitted
dataclass
KnownTransitionOmitted(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())
KnownTransitionOmittedLayout
dataclass
KnownTransitionOmittedLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 8.0, end_arrowhead_width: float = 15.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)
Bases: ReactionLayout, _ReactionNodeMixin
Class for known transition omitted layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_bbox
Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
end_arrowhead_length
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_length
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
LogicArcLayout
dataclass
LogicArcLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = None, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)
Bases: CellDesignerSingleHeadedArc
Class for logic arc layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
Modification
dataclass
Modification(*, id_: str = make_uuid4_as_str(), residue: ModificationResidue | ModificationSite | None = None, state: ModificationState | None = None)
ModificationLayout
dataclass
ModificationLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 16.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 16.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None)
Bases: _SimpleNodeMixin, CellDesignerNode
Class for modification layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
label_center
label_center() -> Point
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
ModificationResidue
dataclass
ModificationSite
dataclass
ModificationState
Bases: Enum
Class for modification states
Modulation
dataclass
Modulation(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
Bases: KnownOrUnknownModulation
Class for modulations
ModulationLayout
dataclass
ModulationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 8.0, arrowhead_width: float = 15.0)
Bases: CellDesignerSingleHeadedArc
Class for modulation layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
Modulator
dataclass
Modulator(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)
NegativeInfluence
dataclass
NegativeInfluence(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
NotGate
dataclass
NotGate(*, id_: str = make_uuid4_as_str(), inputs: frozenset[Species] = frozenset())
NotGateLayout
dataclass
NotGateLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 15.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 15.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None)
Bases: _SimpleNodeMixin, _TextMixin, CellDesignerNode
Class for not gate layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
label_center
label_center() -> Point
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
OrGate
dataclass
OrGate(*, id_: str = make_uuid4_as_str(), inputs: frozenset[Species] = frozenset())
OrGateLayout
dataclass
OrGateLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 15.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 15.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None)
Bases: _SimpleNodeMixin, _TextMixin, CellDesignerNode
Class for or gate layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
label_center
label_center() -> Point
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
OvalCompartmentLayout
dataclass
OvalCompartmentLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 16.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 16.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, inner_fill: NoneValueType | Color | None = white, inner_stroke: NoneValueType | Color | None = black, inner_stroke_width: float | None = 1.0, sep: float = 12.0)
Bases: _SimpleNodeMixin, CellDesignerNode
Class for oval compartment layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
label_center
label_center() -> Point
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
Phenotype
dataclass
PhenotypeLayout
dataclass
PhenotypeLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, angle: float = 60.0)
Bases: _MultiNodeMixin, CellDesignerNode
Class for phenotype layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
angle |
float
|
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
class-attribute
instance-attribute
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/celldesigner/core.py
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/celldesigner/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/celldesigner/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/celldesigner/core.py
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/celldesigner/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/celldesigner/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/celldesigner/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/celldesigner/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/celldesigner/core.py
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/celldesigner/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/celldesigner/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/celldesigner/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/celldesigner/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/celldesigner/core.py
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/celldesigner/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/celldesigner/core.py
PhysicalStimulation
dataclass
PhysicalStimulation(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
PhysicalStimulationLayout
dataclass
PhysicalStimulationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)
Bases: CellDesignerSingleHeadedArc
Class for physical stimulation layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
PhysicalStimulator
dataclass
PhysicalStimulator(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)
PositiveInfluence
dataclass
PositiveInfluence(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
PositiveInfluenceLayout
dataclass
PositiveInfluenceLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = NoneValue, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 2.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)
Bases: CellDesignerSingleHeadedArc
Class for positive influence layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
Product
dataclass
ProductionLayout
dataclass
ProductionLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = black, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 8.0, arrowhead_width: float = 15.0)
Bases: CellDesignerSingleHeadedArc
Class for production layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
Protein
dataclass
Protein(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: ProteinTemplate, modifications: frozenset[Modification] = frozenset(), structural_states: frozenset[StructuralState] = frozenset())
ProteinBindingDomain
dataclass
ProteinTemplate
dataclass
ProteinTemplate(*, id_: str = make_uuid4_as_str(), name: str, modification_residues: frozenset[ModificationResidue] = frozenset())
RNA
dataclass
RNA(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: RNATemplate, modifications: frozenset[Modification] = frozenset())
RNALayout
dataclass
RNALayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, angle: float = 45.0)
Bases: _MultiNodeMixin, CellDesignerNode
Class for RNA layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
angle |
float
|
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
class-attribute
instance-attribute
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/celldesigner/core.py
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/celldesigner/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/celldesigner/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/celldesigner/core.py
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/celldesigner/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/celldesigner/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/celldesigner/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/celldesigner/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/celldesigner/core.py
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/celldesigner/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/celldesigner/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/celldesigner/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/celldesigner/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/celldesigner/core.py
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/celldesigner/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/celldesigner/core.py
RNATemplate
dataclass
RNATemplate(*, id_: str = make_uuid4_as_str(), name: str, regions: frozenset[ModificationSite | CodingRegion | ProteinBindingDomain] = frozenset())
Reactant
dataclass
Reaction
dataclass
Reaction(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())
Receptor
dataclass
Receptor(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: ReceptorTemplate, modifications: frozenset[Modification] = frozenset(), structural_states: frozenset[StructuralState] = frozenset())
ReceptorLayout
dataclass
ReceptorLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, vertical_truncation: float = 0.1)
Bases: _MultiNodeMixin, CellDesignerNode
Class for receptor layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
Return the east anchor of the node
Source code in src/momapy/celldesigner/core.py
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/celldesigner/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/celldesigner/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
Return the north anchor of the node
Source code in src/momapy/celldesigner/core.py
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/celldesigner/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/celldesigner/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/celldesigner/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/celldesigner/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
Return the south anchor of the node
Source code in src/momapy/celldesigner/core.py
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/celldesigner/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/celldesigner/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/celldesigner/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/celldesigner/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
Return the west anchor of the node
Source code in src/momapy/celldesigner/core.py
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/celldesigner/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/celldesigner/core.py
ReceptorTemplate
dataclass
ReceptorTemplate(*, id_: str = make_uuid4_as_str(), name: str, modification_residues: frozenset[ModificationResidue] = frozenset())
RectangleCompartmentLayout
dataclass
RectangleCompartmentLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 16.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 16.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, inner_fill: NoneValueType | Color | None = white, inner_rounded_corners: float = 10.0, inner_stroke: NoneValueType | Color | None = black, inner_stroke_width: float | None = 1.0, rounded_corners: float = 10.0, sep: float = 12.0)
Bases: _SimpleNodeMixin, CellDesignerNode
Class for rectangle compartment layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
label_center
label_center() -> Point
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
Region
dataclass
RegulatoryRegion
dataclass
SimpleMolecule
dataclass
SimpleMoleculeLayout
dataclass
SimpleMoleculeLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1)
Bases: _MultiNodeMixin, CellDesignerNode
Class for simple chemical layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
Species
dataclass
SpeciesTemplate
dataclass
StateTransition
dataclass
StateTransition(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())
StateTransitionLayout
dataclass
StateTransitionLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 8.0, end_arrowhead_width: float = 15.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)
Bases: ReactionLayout, _ReactionNodeMixin
Class for state transition layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_bbox
Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
end_arrowhead_length
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_length
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
StructuralState
dataclass
StructuralStateLayout
dataclass
StructuralStateLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 16.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 50.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None)
Bases: _SimpleNodeMixin, CellDesignerNode
Class for structural states layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
label_center
label_center() -> Point
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
Transcription
dataclass
Transcription(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())
TranscriptionLayout
dataclass
TranscriptionLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4, 2, 4, 2, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 8.0, end_arrowhead_width: float = 15.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)
Bases: ReactionLayout, _ReactionNodeMixin
Class for transcription layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_bbox
Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
end_arrowhead_length
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_length
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
TranscriptionStartingSiteL
dataclass
TranscriptionStartingSiteR
dataclass
Translation
dataclass
Translation(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())
TranslationLayout
dataclass
TranslationLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4, 2, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 8.0, end_arrowhead_width: float = 15.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)
Bases: ReactionLayout, _ReactionNodeMixin
Class for translation layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_bbox
Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
end_arrowhead_length
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_length
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
Transport
dataclass
Transport(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())
TransportLayout
dataclass
TransportLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_bar_height: float = 8.0, end_arrowhead_sep: float = 5.0, end_arrowhead_triangle_height: float = 8.0, end_arrowhead_triangle_width: float = 15.0, start_arrowhead_bar_height: float = 8.0, start_arrowhead_sep: float = 4.0, start_arrowhead_triangle_height: float = 8.0, start_arrowhead_triangle_width: float = 15.0)
Bases: ReactionLayout, _ReactionNodeMixin
Class for transport layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_bbox
Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
end_arrowhead_length
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_length
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
Trigger
dataclass
Trigger(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)
Triggering
dataclass
Triggering(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
TriggeringLayout
dataclass
TriggeringLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_bar_height: float = 8.0, arrowhead_sep: float = 5.0, arrowhead_triangle_height: float = 10.0, arrowhead_triangle_width: float = 15.0)
Bases: CellDesignerSingleHeadedArc
Class for triggering layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
TruncatedProtein
dataclass
TruncatedProtein(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, compartment: Compartment | None = None, hypothetical: bool = False, active: bool = False, homomultimer: int = 1, template: TruncatedProteinTemplate, modifications: frozenset[Modification] = frozenset(), structural_states: frozenset[StructuralState] = frozenset())
TruncatedProteinLayout
dataclass
TruncatedProteinLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1, rounded_corners: float = 15.0, vertical_truncation: float = 0.4, horizontal_truncation: float = 0.2)
Bases: _MultiNodeMixin, CellDesignerNode
Class for truncated protein layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
TruncatedProteinTemplate
dataclass
TruncatedProteinTemplate(*, id_: str = make_uuid4_as_str(), name: str, modification_residues: frozenset[ModificationResidue] = frozenset())
Truncation
dataclass
Truncation(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())
TruncationLayout
dataclass
TruncationLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = white, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 10.0, end_arrowhead_sep: float = 2.0, end_arrowhead_width: float = 10.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)
Bases: ReactionLayout, _ReactionNodeMixin
Class for truncation layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_bbox
Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
end_arrowhead_length
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_length
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
Unknown
dataclass
UnknownCatalysis
dataclass
UnknownCatalysis(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
UnknownCatalysisLayout
dataclass
UnknownCatalysisLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 7.0, arrowhead_width: float = 7.0)
Bases: CellDesignerSingleHeadedArc
Class for unknown catalysis layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
UnknownCatalyzer
dataclass
UnknownCatalyzer(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)
UnknownGate
dataclass
UnknownGate(*, id_: str = make_uuid4_as_str(), inputs: frozenset[Species] = frozenset())
UnknownGateLayout
dataclass
UnknownGateLayout(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, filter: NoneValueType | Filter | None = None, height: float = 15.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 15.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None)
Bases: _SimpleNodeMixin, _TextMixin, CellDesignerNode
Class for unknown gate layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
label_center |
Return the label center anchor of the node |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
label_center
label_center() -> Point
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
UnknownInhibition
dataclass
UnknownInhibition(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
UnknownInhibitionLayout
dataclass
UnknownInhibitionLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 3.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = None, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0)
Bases: CellDesignerSingleHeadedArc
Class for unknown inhibition layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
UnknownInhibitor
dataclass
UnknownInhibitor(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)
UnknownLayout
dataclass
UnknownLayout(stroke_width: float | None = 1.25, offset: float = 3.0, subunits_stroke: tuple[NoneValueType | Color] | None = None, subunits_stroke_width: tuple[NoneValueType | float] | None = None, subunits_stroke_dasharray: tuple[NoneValueType | tuple[float]] | None = None, subunits_stroke_dashoffset: tuple[float] | None = None, subunits_fill: tuple[NoneValueType | Color] | None = None, subunits_transform: tuple[NoneValueType | tuple[Transformation]] | None = None, subunits_filter: tuple[NoneValueType | Filter] | None = None, *, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, fill: NoneValueType | Color | None = gray, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = NoneValue, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, active: bool = False, active_fill: NoneValueType | Color | None = NoneValue, active_filter: NoneValueType | Filter | None = None, active_sep: float = 4.0, active_stroke: NoneValueType | Color | None = black, active_stroke_dasharray: NoneValueType | tuple[float] | None = (4, 2), active_stroke_dashoffset: float | None = None, active_stroke_width: float | None = 1.0, active_transform: NoneValueType | tuple[Transformation] | None = None, n: int = 1)
Bases: _MultiNodeMixin, CellDesignerNode
Class for unknown species layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
angle |
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
bbox |
Compute and return the bounding box of the group layout element |
border |
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
center |
Return the center anchor of the node |
childless |
Return a copy of the node with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
east |
Return the east anchor of the node |
east_north_east |
Return the east north east anchor of the node |
east_south_east |
Return the east south east west anchor of the node |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
north |
Return the north anchor of the node |
north_east |
Return the north east anchor of the node |
north_north_east |
Return the north north east anchor of the node |
north_north_west |
Return the north north west anchor of the node |
north_west |
Return the north west anchor of the node |
self_angle |
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal. |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_border |
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. |
self_children |
Return the self children of the node. A node has unique child that is its label |
self_drawing_elements |
Return the node's own drawing elements |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
size |
Return the size of the node |
south |
Return the south anchor of the node |
south_east |
Return the south east anchor of the node |
south_south_east |
Return the south south east anchor of the node |
south_south_west |
Return the south south west anchor of the node |
south_west |
Return the south west anchor of the node |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
west |
Return the west anchor of the node |
west_north_west |
Return the west north west anchor of the node |
west_south_west |
Return the west south west anchor of the node |
Attributes:
| Name | Type | Description |
|---|---|---|
x |
float
|
Return the x coordinate of the node |
y |
float
|
Return the y coordinate of the node |
anchor_point
anchor_point(anchor_name: str) -> Point
angle
angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
border
Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
center
center() -> Point
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
east
east() -> Point
east_north_east
east_north_east() -> Point
Return the east north east anchor of the node
Source code in src/momapy/core.py
east_south_east
east_south_east() -> Point
Return the east south east west anchor of the node
Source code in src/momapy/core.py
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
north
north() -> Point
north_east
north_east() -> Point
Return the north east anchor of the node
Source code in src/momapy/core.py
north_north_east
north_north_east() -> Point
Return the north north east anchor of the node
Source code in src/momapy/core.py
north_north_west
north_north_west() -> Point
Return the north north west anchor of the node
Source code in src/momapy/core.py
north_west
north_west() -> Point
Return the north west anchor of the node
Source code in src/momapy/core.py
self_angle
self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point
Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
Source code in src/momapy/core.py
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_border
Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
self_children
self_children() -> list[LayoutElement]
Return the self children of the node. A node has unique child that is its label
self_drawing_elements
self_drawing_elements() -> list[DrawingElement]
Return the node's own drawing elements
Source code in src/momapy/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size
south
south() -> Point
south_east
south_east() -> Point
Return the south east anchor of the node
Source code in src/momapy/core.py
south_south_east
south_south_east() -> Point
Return the south south east anchor of the node
Source code in src/momapy/core.py
south_south_west
south_south_west() -> Point
Return the south south west anchor of the node
Source code in src/momapy/core.py
south_west
south_west() -> Point
Return the south west anchor of the node
Source code in src/momapy/core.py
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
west
west() -> Point
west_north_west
west_north_west() -> Point
Return the west north west anchor of the node
Source code in src/momapy/core.py
west_south_west
west_south_west() -> Point
Return the west south west anchor of the node
Source code in src/momapy/core.py
UnknownModulation
dataclass
UnknownModulation(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
Bases: KnownOrUnknownModulation
Class for unknown modulations
UnknownModulationLayout
dataclass
UnknownModulationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 8.0, arrowhead_width: float = 15.0)
Bases: CellDesignerSingleHeadedArc
Class for unknown modulation layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
UnknownModulator
dataclass
UnknownModulator(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, referred_species: Species | BooleanLogicGate)
UnknownNegativeInfluence
dataclass
UnknownNegativeInfluence(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
UnknownPhysicalStimulation
dataclass
UnknownPhysicalStimulation(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
UnknownPhysicalStimulationLayout
dataclass
UnknownPhysicalStimulationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)
Bases: CellDesignerSingleHeadedArc
Class for unknown physical stimulation layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
UnknownPositiveInfluence
dataclass
UnknownPositiveInfluence(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
UnknownPositiveInfluenceLayout
dataclass
UnknownPositiveInfluenceLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = NoneValue, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 2.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)
Bases: CellDesignerSingleHeadedArc
Class for unknown positive influence layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
UnknownTransition
dataclass
UnknownTransition(*, id_: str = make_uuid4_as_str(), name: str | None = None, sbo_term: SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: Compartment | None = None, reactants: frozenset[Reactant] = frozenset(), products: frozenset[Product] = frozenset(), modifiers: frozenset[KnownOrUnknownModulator] = frozenset())
UnknownTransitionLayout
dataclass
UnknownTransitionLayout(*, left_connector_fraction: float = 0.4, right_connector_fraction: float = 0.6, reaction_node_height: float = 10.0, reaction_node_width: float = 10.0, reaction_node_segment: int = 1, reaction_node_stroke: NoneValueType | Color | None = black, reaction_node_stroke_width: float | None = 1.0, reaction_node_stroke_dasharray: NoneValueType | tuple[float] | None = None, reaction_node_stroke_dashoffset: float | None = None, reaction_node_fill: NoneValueType | Color | None = white, reaction_node_transform: NoneValueType | tuple[Transformation] | None = None, reaction_node_filter: NoneValueType | Filter | None = None, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 2.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 2.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, end_arrowhead_fill: NoneValueType | Color | None = black, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_stroke_width: float | None = 1.0, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_fill: NoneValueType | Color | None = black, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke: NoneValueType | Color | None = black, start_arrowhead_stroke_dasharray: NoneValueType | tuple[float] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_stroke_width: float | None = 1.0, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, reversible: bool = False, end_arrowhead_height: float = 8.0, end_arrowhead_width: float = 15.0, start_arrowhead_height: float = 8.0, start_arrowhead_width: float = 15.0)
Bases: ReactionLayout, _ReactionNodeMixin
Class for unknown transition layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_arrowhead_base |
Return the base anchor point of the double-headed arc end arrowhead |
end_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
end_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. |
end_arrowhead_length |
Return the length of the double-headed arc end arrowhead |
end_arrowhead_tip |
Return the tip anchor point of the double-headed arc end arrowhead |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the double-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_arrowhead_base |
Return the base anchor point of the double-headed arc start arrowhead |
start_arrowhead_bbox |
Return the bounding box of the double-headed arc start arrowhead |
start_arrowhead_border |
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. |
start_arrowhead_drawing_elements |
Return the drawing elements of the double-headed arc start arrowhead |
start_arrowhead_length |
Return the length of the double-headed arc start arrowhead |
start_arrowhead_tip |
Return the tip anchor point of the double-headed arc start arrowhead |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_arrowhead_base
end_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_bbox
Return the bounding box of the double-headed arc start arrowhead
end_arrowhead_border
Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
end_arrowhead_length
Return the length of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_arrowhead_tip
end_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc end arrowhead
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the double-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_arrowhead_base
start_arrowhead_base() -> Point
Return the base anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_bbox
start_arrowhead_bbox() -> Bbox
Return the bounding box of the double-headed arc start arrowhead
start_arrowhead_border
start_arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
start_arrowhead_drawing_elements
start_arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_length
Return the length of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_arrowhead_tip
start_arrowhead_tip() -> Point
Return the tip anchor point of the double-headed arc start arrowhead
Source code in src/momapy/core.py
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element
Source code in src/momapy/core.py
UnknownTriggering
dataclass
UnknownTriggering(*, id_: str = make_uuid4_as_str(), source: Species | BooleanLogicGate, target: Species | None)
UnknownTriggeringLayout
dataclass
UnknownTriggeringLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float] | None = (12, 4), path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.0, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | BezierCurve | EllipticalArc] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.0, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_bar_height: float = 8.0, arrowhead_sep: float = 5.0, arrowhead_triangle_height: float = 10.0, arrowhead_triangle_width: float = 15.0)
Bases: CellDesignerSingleHeadedArc
Class for unknown triggering layouts
Methods:
| Name | Description |
|---|---|
anchor_point |
Return an anchor point of the layout element |
arrowhead_base |
Return the arrowhead base anchor point of the single-headed arc |
arrowhead_bbox |
Return the bounding box of the single-headed arc arrowhead |
arrowhead_border |
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. |
arrowhead_drawing_elements |
Return the drawing elements of the single-headed arc arrowhead |
arrowhead_length |
Return the length of the single-headed arc arrowhead |
arrowhead_tip |
Return the arrowhead tip anchor point of the single-headed arc |
bbox |
Compute and return the bounding box of the group layout element |
childless |
Return a copy of the arc with no children |
children |
Return the children of the group layout. |
contains |
Return |
descendants |
Return the descendants of the layout element |
drawing_elements |
Return the drawing elements of the group layout. |
end_point |
Return the ending point of the arc |
equals |
Return |
flattened |
Return a list containing copy of the layout element with no children and all its descendants with no children |
fraction |
Return the position and angle on the arc at a given fraction (of the total arc length) |
length |
Return the total length of the arc path |
path_drawing_elements |
Return the drawing elements of the single-headed arc path |
points |
Return the points of the arc path |
self_bbox |
Compute and return the bounding box of the self drawing element of the group layout |
self_children |
Return the self children of the arc |
self_drawing_elements |
Return the self drawing elements of the single-headed arc |
self_to_shapely |
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout |
start_point |
Return the starting point of the arc |
to_shapely |
Return a shapely collection of geometries reproducing the drawing elements of the layout element |
anchor_point
anchor_point(anchor_name: str) -> Point
arrowhead_base
arrowhead_base() -> Point
Return the arrowhead base anchor point of the single-headed arc
Source code in src/momapy/core.py
arrowhead_border
arrowhead_border(point) -> Point
Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned
Source code in src/momapy/core.py
arrowhead_drawing_elements
arrowhead_drawing_elements() -> list[DrawingElement]
Return the drawing elements of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_length
Return the length of the single-headed arc arrowhead
Source code in src/momapy/core.py
arrowhead_tip
arrowhead_tip() -> Point
Return the arrowhead tip anchor point of the single-headed arc
Source code in src/momapy/core.py
bbox
bbox() -> Bbox
Compute and return the bounding box of the group layout element
Source code in src/momapy/core.py
childless
children
children() -> list[LayoutElement]
Return the children of the group layout.
These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)
Source code in src/momapy/core.py
contains
contains(other: LayoutElement) -> bool
Return true if another layout element is a descendant of the layout element, false otherwise
drawing_elements
drawing_elements() -> list[DrawingElement]
Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
Source code in src/momapy/core.py
end_point
end_point() -> Point
equals
equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool
Return true if the layout element is equal to another layout element, false otherwise
Source code in src/momapy/core.py
flattened
flattened() -> list[LayoutElement]
Return a list containing copy of the layout element with no children and all its descendants with no children
Source code in src/momapy/core.py
fraction
fraction(fraction: float) -> tuple[Point, float]
Return the position and angle on the arc at a given fraction (of the total arc length)
Source code in src/momapy/core.py
length
path_drawing_elements
path_drawing_elements() -> list[Path]
Return the drawing elements of the single-headed arc path
Source code in src/momapy/core.py
points
points() -> list[Point]
self_bbox
self_bbox() -> Bbox
Compute and return the bounding box of the self drawing element of the group layout
self_children
self_children() -> list[LayoutElement]
self_drawing_elements
Return the self drawing elements of the single-headed arc
Source code in src/momapy/celldesigner/core.py
self_to_shapely
Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point
start_point() -> Point
to_shapely
Return a shapely collection of geometries reproducing the drawing elements of the layout element